It looks like this is due to the way Gmail structures its IMAP folders, which all get monitored by default for new mail notifications in the /e/OS Mail app. To make it send only one notification I configured the Notifications settings in the Mail app for each Gmail account and changed Notification folders from “All” to “Only 1st Class folders”.
@Manoj It might be good to move this thread to Settings or Applications because it’s a general /e/OS quirk that is not specific to a certain device.